It’s beginning to look like 2013 will go down in the history books as the coffee world’s annus horribilis.

It’s the Year of Rust, or more specifically, Hemileia vastatrix, the coffee rust fungus. While never a welcome sight, the telltale orange dust can, in a normal year, typically be described as seasonal, commonplace and mild. The adjectives that are being used in coffee rust conversations this year conjure up a very different reality: severe, devastating, crisis.

The rust compromises the plant’s ability to photosynthesize. A severe outbreak can lead to defoliation and die-off at the plantation level. Losses are projected to approach 50 percent of the 2013-2014 harvest in Guatemala, Colombia, Honduras and Costa Rica. Guatemala’s National Coffee Association has declared a state of emergency due to the spread of the disease.

In a New York Times piece on the crisis, experts debate whether it is changes in farming practices or the effects of climate change that are primarily responsible for the degree and severity of the current outbreak.

The either/or nature of the debate may be a false dichotomy. Both can (and likely do) play a role. Climate change sets the scene with changing rainfall patterns and the generally wetter conditions that support the growth of the fungus. The use of modern farming practices throws two additional complications into the mix: reduced genetic diversity and the eradication of natural biological controls.

So, we have here a recipe for disaster: Take large swaths of deforested land, plant crops with little to no genetic diversity, add in some pesticides to remove the rust’s natural enemy and allow for a few years of wetter conditions.

Coffee rust is not the only coffee-related disaster climate change has up its sleeve. Scientists working with climate change models predict that changing conditions may lead to the extinction of indigenous Arabica coffee, due to a significant reduction in bioclimatically suitable habitat. The loss of wild plants represents yet another blow to genetic diversity, as those wild plants are the best source for finding varieties that are resistant to new pests and other future threats.

For a short primer on supporting coffee farmers who use practices that support environmental and genetic diversity, see our article on Bird Friendly Coffee.